Hey everyone,

We have a total RNA data set of paired end reads from soil samples and followed our pipeline to get mRNA, rRNA and count tables for each. But now the question is: Can we create a transcriptome per OTU and map the mRNA reads against? Basically identifying which rRNA contigs are actively "expressing" which mRNA contigs? I did that before with transcriptomics, but that was one species per samples and now we talk about >3k microbial rRNA contigs.

Maybe the answer is obvious, and there are tools such as MEGAN, but I wanted to ask the community what is being used at the moment, that only works with the metatranscriptomic dataset, NOT MAGs!

Curious to read your answer! :-)